Are red or green peppers more nutritious? Ask anyone this question and almost always, the answer you get is that red are the winner. The truth is that they're actually the loser in terms of total antioxidant content!
Fresh red peppers calculate out to have an ORAC value of 821. Green peppers are 935. It may not be a dramatic difference, but it's something to keep in mind if you've been choosing red solely for nutritional value. That said, there are certain types of phytonutrients found in the red (plus orange and yellow) skins that you won't get from green (or you get very little of).
USDA Database for the Oxygen Radical Absorbance Capacity (ORAC) of Selected Foods, Release 2 - Prepared by Nutrient Data Laboratory, Beltsville Human Nutrition Research Center (BHNRC), Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA) - May 2010